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cgob / codonDT_snakemake

Ribo-DT is a snakemake pipeline to infer single-codon and codon-pair dwell times as well as gene flux from ribosome profiling data using generalized linear model (GLM) with negative binomial noise model (Gobet et al., PNAS, 2020).
MIT License
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Code running to completion, but not producing output files #6

Open agoldkamp opened 2 years ago

agoldkamp commented 2 years ago

Hello, I am currently using codonDT_snakemake to analyze my ribosome profiling data. The code will run without any errors and finish, but I am unable to find any output files. I am assuming the output files should be within the /Data/ directory? Any suggestions on how I can resolve this?

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cgob commented 2 years ago

Hello, Do you get any folders or files created in the "workdir" directory that you defined in the "config.yaml" file?

Cédric

agoldkamp commented 2 years ago

Hi, I am not getting any folders or files created in the working directory. I just redownloaded. I initially got this error, so I had added "/Cow/genome" within the "references" directory. I am assuming this is what is causing the issue because I believe the program should generate these folders on its own?

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agoldkamp commented 2 years ago

Hi again,

It looks like the error was on my end. I ran the default data set which successfully ran and produced output files. I then added my fastq files to the "Data/Raw" directory, and removed the --touch command and it started to produce output files.

However, it failed for one of the samples (Liver_2) at the "findAsite" step.

Screen Shot 2022-01-17 at 12 06 20 PM

I apologize for all of the questions. I think this tool could be very beneficial for our project and appreciate any feedback!

Thank you, Anna

cgob commented 1 year ago

Dear Anna,

Sorry for the late reply. Did you solve your issue ? Were you able to run the pipeline on your data successfully?

Best,

Cédric